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CHECK report for DEDS on tokay1

This page was generated on 2018-04-12 13:17:40 -0400 (Thu, 12 Apr 2018).

Package 341/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEDS 1.52.0
Yuanyuan Xiao
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/DEDS
Branch: RELEASE_3_6
Last Commit: 5520565
Last Changed Date: 2017-10-30 12:39:03 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DEDS
Version: 1.52.0
Command: rm -rf DEDS.buildbin-libdir DEDS.Rcheck && mkdir DEDS.buildbin-libdir DEDS.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DEDS.buildbin-libdir DEDS_1.52.0.tar.gz >DEDS.Rcheck\00install.out 2>&1 && cp DEDS.Rcheck\00install.out DEDS-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DEDS.buildbin-libdir --install="check:DEDS-install.out" --force-multiarch --no-vignettes --timings DEDS_1.52.0.tar.gz
StartedAt: 2018-04-11 23:23:43 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:24:39 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 56.5 seconds
RetCode: 0
Status:  OK  
CheckDir: DEDS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DEDS.buildbin-libdir DEDS.Rcheck && mkdir DEDS.buildbin-libdir DEDS.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DEDS.buildbin-libdir DEDS_1.52.0.tar.gz >DEDS.Rcheck\00install.out 2>&1 && cp DEDS.Rcheck\00install.out DEDS-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DEDS.buildbin-libdir --install="check:DEDS-install.out" --force-multiarch --no-vignettes --timings DEDS_1.52.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/DEDS.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DEDS/DESCRIPTION' ... OK
* this is package 'DEDS' version '1.52.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'DEDS' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
deds.stat.linkC: warning in matrix(res$t, byrow = FALSE, nc = newX$nT):
  partial argument match of 'nc' to 'ncol'
sam.multiclass.func: warning in matrix(nr = nrow(X), nc = B): partial
  argument match of 'nr' to 'nrow'
sam.multiclass.func: warning in matrix(nr = nrow(X), nc = B): partial
  argument match of 'nc' to 'ncol'
sam.oneclass.func: warning in matrix(nr = nrow(X), nc = B): partial
  argument match of 'nr' to 'nrow'
sam.oneclass.func: warning in matrix(nr = nrow(X), nc = B): partial
  argument match of 'nc' to 'ncol'
sam.twoclass.func: warning in matrix(nr = nrow(X), nc = B): partial
  argument match of 'nr' to 'nrow'
sam.twoclass.func: warning in matrix(nr = nrow(X), nc = B): partial
  argument match of 'nc' to 'ncol'
* checking Rd files ... NOTE
prepare_Rd: comp.fdr.Rd:52-54: Dropping empty section \details
prepare_Rd: deds.pval.Rd:65-68: Dropping empty section \examples
prepare_Rd: hist.DEDS.Rd:47-50: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/DEDS.buildbin-libdir/DEDS/libs/i386/DEDS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/DEDS.Rcheck/00check.log'
for details.



Installation output

DEDS.Rcheck/00install.out


install for i386

* installing *source* package 'DEDS' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c deds.c -o deds.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c distance.c -o distance.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c input.c -o input.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c manip.c -o manip.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c random.c -o random.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c sampling.c -o sampling.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c stat_fun.c -o stat_fun.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o DEDS.dll tmp.def deds.o distance.o input.o manip.o random.o sampling.o stat_fun.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/DEDS.buildbin-libdir/DEDS/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'DEDS'
    finding HTML links ... done
    ApoA1                                   html  
    DEDS-internal                           html  
    affySpikeIn                             html  
    aggregateFun                            html  
    comp.B                                  html  
    comp.F                                  html  
    comp.FC                                 html  
    comp.SAM                                html  
    comp.adjp                               html  
    comp.ebayes                             html  
    comp.fdr                                html  
    comp.modF                               html  
    comp.modt                               html  
    comp.stat                               html  
    comp.t                                  html  
    comp.unadjp                             html  
    deds.chooseTest                         html  
    deds.class                              html  
    deds.genExtra                           html  
    deds.pval                               html  
    deds.stat                               html  
    deds.stat.linkC                         html  
    hist.DEDS                               html  
    pairs.DEDS                              html  
    qqnorm.DEDS                             html  
    topgenes                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'DEDS' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c deds.c -o deds.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c distance.c -o distance.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c input.c -o input.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c manip.c -o manip.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c random.c -o random.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c sampling.c -o sampling.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c stat_fun.c -o stat_fun.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o DEDS.dll tmp.def deds.o distance.o input.o manip.o random.o sampling.o stat_fun.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/DEDS.buildbin-libdir/DEDS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DEDS' as DEDS_1.52.0.zip
* DONE (DEDS)
In R CMD INSTALL
In R CMD INSTALL

Tests output


Example timings

DEDS.Rcheck/examples_i386/DEDS-Ex.timings

nameusersystemelapsed
aggregateFun0.060.000.06
comp.B0.020.000.02
comp.F0.140.000.14
comp.FC0.010.000.02
comp.SAM0.380.000.37
comp.adjp0.040.000.05
comp.ebayes000
comp.fdr0.050.000.05
comp.modF000
comp.modt000
comp.stat0.010.000.02
comp.t0.030.000.03
comp.unadjp0.020.000.01
deds.chooseTest1.980.052.03
deds.genExtra000
deds.stat1.770.001.77
deds.stat.linkC0.020.000.01
pairs.DEDS0.210.000.22
qqnorm.DEDS0.070.000.07
topgenes0.040.000.04

DEDS.Rcheck/examples_x64/DEDS-Ex.timings

nameusersystemelapsed
aggregateFun0.080.010.09
comp.B0.010.000.02
comp.F0.160.020.18
comp.FC0.030.000.03
comp.SAM0.940.000.93
comp.adjp0.060.000.07
comp.ebayes0.010.000.01
comp.fdr0.050.000.05
comp.modF000
comp.modt0.010.000.02
comp.stat000
comp.t0.050.000.05
comp.unadjp000
deds.chooseTest2.880.002.88
deds.genExtra000
deds.stat2.340.002.34
deds.stat.linkC0.030.000.03
pairs.DEDS0.410.000.41
qqnorm.DEDS0.060.010.08
topgenes0.070.000.06